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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 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'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ), 'gf_id' => 'HOM05D001122', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001122' ), 'data_identifier' => 'HOM05D001122', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001122', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '549', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14660' => 'bna', 'A02p18690' => 'bna', 'A03p21230' => 'bna', 'A03p22780' => 'bna', 'A03p48470' => 'bna', 'A04p13670' => 'bna', 'A04p29360' => 'bna', 'A04p30950' => 'bna', 'A08p02770' => 'bna', 'A09p44840' => 'bna', 'A09p44880' => 'bna', 'A09p49250' => 'bna', 'A09p55280' => 'bna', 'Aa31LG5G11660' => 'aar', 'Aa31LG5G19040' => 'aar', 'Aa31LG5G24080' => 'aar', 'Aa31sc463G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1874' => 'aag', 'Actinidia11523' => 'ach', 'Actinidia11525' => 'ach', 'Actinidia20784' => 'ach', 'Actinidia29048' => 'ach', 'Actinidia29745' => 'ach', 'Actinidia34818' => 'ach', 'Ah.15g090210' => 'amhyb', 'Ah.15g090230' => 'amhyb', 'AL4G35300' => 'aly', 'AL4G35550' => 'aly', 'AL4G35590' => 'aly', 'AL4G38330' => 'aly', 'AL5G32170' => 'aly', 'AL5G32190' => 'aly', 'AL5G37590' => 'aly', 'AL6G10230' => 'aly', 'AL96U10020' => 'aly', 'AL96U10050' => 'aly', 'Aqoxy2G00741' => 'aox', 'Aqoxy2G00742' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5K0G3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJL1FY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF4ABA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV71QX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7KKGP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH7SIY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0IKGX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U3MJA7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y8SUHG' => 'arhy', 'AT2G38370' => 'ath', 'AT2G40480' => 'ath', 'AT3G51720' => 'ath', 'AT3G51730' => 'ath', 'AT3G56270' => 'ath', 'AT5G01800' => 'ath', 'ATR0681G065' => 'atr', 'ATR0681G215' => 'atr', 'ATR0752G144' => 'atr', 'Atru.chr12.149' => 'acertr', 'Atru.chr8.2373' => 'acertr', 'Atru.chr8.2374' => 'acertr', 'AUR62006350' => 'cqu', 'AUR62006354' => 'cqu', 'AUR62012351' => 'cqu', 'AUR62022997' => 'cqu', 'AUR62029682' => 'cqu', 'AUR62029684' => 'cqu', 'AUR62043567' => 'cqu', 'BcaB01g00008' => 'bca', 'BcaB01g00423' => 'bca', 'BcaB01g00424' => 'bca', 'BcaB01g00426' => 'bca', 'BcaB01g00484' => 'bca', 'BcaB01g00491' => 'bca', 'BcaB01g00492' => 'bca', 'BcaB01g00493' => 'bca', 'BcaB01g03536' => 'bca', 'BcaB01g03692' => 'bca', 'BcaB01g03695' => 'bca', 'BcaB01g03698' => 'bca', 'BcaB01g03699' => 'bca', 'BcaB06g29047' => 'bca', 'BcaB06g29147' => 'bca', 'BcaB08g35450' => 'bca', 'BcaC01g05397' => 'bca', 'BcaC01g05545' => 'bca', 'BcaC01g05777' => 'bca', 'BcaC02g07470' => 'bca', 'BcaC02g07472' => 'bca', 'BcaC02g07473' => 'bca', 'BcaC02g10693' => 'bca', 'BcaC04g22401' => 'bca', 'BcaC06g31953' => 'bca', 'BcaC06g33004' => 'bca', 'BcaC06g33346' => 'bca', 'BcaC07g37682' => 'bca', 'BcaC07g37683' => 'bca', 'BcaC07g39945' => 'bca', 'BcaNung03300' => 'bca', 'BcaNung03305' => 'bca', 'BolC1t02088H' => 'bol', 'BolC3t14632H' => 'bol', 'BolC3t14902H' => 'bol', 'BolC3t15084H' => 'bol', 'BolC4t24129H' => 'bol', 'BolC4t24130H' => 'bol', 'BolC4t24320H' => 'bol', 'BolC4t28168H' => 'bol', 'BolC4t28336H' => 'bol', 'BolC7t45172H' => 'bol', 'BolC8t48053H' => 'bol', 'BolC8t50306H' => 'bol', 'BolC8t50313H' => 'bol', 'BolC8t50781H' => 'bol', 'BolC9t54877H' => 'bol', 'BolC9t60205H' => 'bol', 'BraA02t06911Z' => 'bra', 'BraA03t11360Z' => 'bra', 'BraA03t11502Z' => 'bra', 'BraA03t13952Z' => 'bra', 'BraA04t16093Z' => 'bra', 'BraA04t18404Z' => 'bra', 'BraA04t18553Z' => 'bra', 'BraA09t39946Z' => 'bra', 'BraA09t39949Z' => 'bra', 'BraA09t40378Z' => 'bra', 'C01p21720' => 'bna', 'C01p35710' => 'bna', 'C03p25110' => 'bna', 'C03p27020' => 'bna', 'C04p26740' => 'bna', 'C04p27770' => 'bna', 'C04p66660' => 'bna', 'C04p68340' => 'bna', 'C07p46560' => 'bna', 'C08p26890' => 'bna', 'C08p26930' => 'bna', 'C08p31600' => 'bna', 'C09p19750' => 'bna', 'C09p74730' => 'bna', 'CAN.G111.30' => 'can', 'CAN.G15.26' => 'can', 'CAN.G484.75' => 'can', 'CAN.G738.7' => 'can', 'CANSAT35G1279' => 'cansat', 'CANSAT35G1567' => 'cansat', 'CARHR132980' => 'chi', 'CARHR135600' => 'chi', 'CARHR161330' => 'chi', 'CARHR161360' => 'chi', 'CARHR166430' => 'chi', 'CARHR184050' => 'chi', 'CARHR229670' => 'chi', 'Carub.0004s2034' => 'cru', 'Carub.0004s2274' => 'cru', 'Carub.0005s1806' => 'cru', 'Carub.0005s1807' => 'cru', 'Carub.0005s2305' => 'cru', 'Carub.0006s0003' => 'cru', 'Ca_06022_v3' => 'car', 'Ca_07747_v3' => 'car', 'Ca_07748_v3' => 'car', 'Ca_15188_v3' => 'car', 'Ca_19773_v3' => 'car', 'Ca_19776_v3' => 'car', 'CBR_g3540' => 'cbr', 'Cc02_g05600' => 'ccan', 'Cc06_g00540' => 'ccan', 'Cc06_g00550' => 'ccan', 'CDE04G1276' => 'cde', 'CDE04G2871' => 'cde', 'CDE05G1998' => 'cde', 'CDE12G0457' => 'cde', 'Cfa001228' => 'cfa', 'Cfa017062' => 'cfa', 'Ciclev10011064m.g' => 'ccl', 'Ciclev10031082m.g' => 'ccl', 'CiPaw.01G304500' => 'cil', 'CiPaw.09G218300' => 'cil', 'CiPaw.09G218500' => 'cil', 'CiPaw.09G218600' => 'cil', 'CiPaw.09G218700' => 'cil', 'CiPaw.10G163900' => 'cil', 'CiPaw.10G164000' => 'cil', 'ClCG04G006470' => 'cla', 'ClCG04G006480' => 'cla', 'ClCG10G022610' => 'cla', 'ClCG11G005750' => 'cla', 'COL.COLO4_30003' => 'col', 'COL.COLO4_30004' => 'col', 'Cpa.g.sc19.90' => 'cpa', 'Cpa.g.sc86.25' => 'cpa', 'Cpa.g.sc86.26' => 'cpa', 'CsaV3_3G033220' => 'csa', 'CsaV3_4G027030' => 'csa', 'CsaV3_4G027040' => 'csa', 'CsaV3_4G027050' => 'csa', 'CsaV3_6G002220' => 'csa', 'CsaV3_UNG105770' => 'csa', 'CsaV3_UNG107770' => 'csa', 'CSS0014462' => 'camsi', 'CSS0020386' => 'camsi', 'CSS0024307' => 'camsi', 'CSS0026092' => 'camsi', 'CSS0030369' => 'camsi', 'CSS0038239' => 'camsi', 'CSS0040395' => 'camsi', 'CSS0043268' => 'camsi', 'CSS0044199' => 'camsi', 'DCAR_010960' => 'dca', 'DCAR_015347' => 'dca', 'DCAR_018655' => 'dca', 'DCAR_028909' => 'dca', 'Dinv10548' => 'din', 'Dinv11389' => 'din', 'Dinv11390' => 'din', 'Dinv11391' => 'din', 'Dinv21822' => 'din', 'Dinv25307' => 'din', 'Dinv25309' => 'din', 'Dinv25315' => 'din', 'Duzib128G1015' => 'dzi', 'Duzib151G0339' => 'dzi', 'Duzib151G1105' => 'dzi', 'Duzib212G0698' => 'dzi', 'Duzib212G0732' => 'dzi', 'Duzib268G0086' => 'dzi', 'ECA232G2170' => 'eca', 'ECA236G4443' => 'eca', 'ECA247G0333' => 'eca', 'ECA248G3012' => 'eca', 'EL10Ac2g04266' => 'bvu', 'EL10Ac7g17055' => 'bvu', 'EL10Ac7g17057' => 'bvu', 'Eucgr.A00686' => 'egr', 'Eucgr.A00687' => 'egr', 'Eucgr.G03122' => 'egr', 'Eucgr.K01273' => 'egr', 'FAN01G1070' => 'fan', 'FAN02G1434' => 'fan', 'FAN02G3784' => 'fan', 'FAN03G2841' => 'fan', 'FAN05G1096' => 'fan', 'FAN05G3468' => 'fan', 'FAN05G4057' => 'fan', 'FAN05G5303' => 'fan', 'FAN06G0201' => 'fan', 'FAN09G1334' => 'fan', 'FAN09G3749' => 'fan', 'FAN14G1450' => 'fan', 'FAN14G3888' => 'fan', 'FvH4_6g10220' => 'fve', 'FvH4_6g10230' => 'fve', 'FvH4_7g25600' => 'fve', 'Glyma.01G131300' => 'gma', 'Glyma.01G131400' => 'gma', 'Glyma.02G259100' => 'gma', 'Glyma.03G037009' => 'gma', 'Glyma.03G037500' => 'gma', 'Glyma.09G277100' => 'gma', 'Glyma.09G277200' => 'gma', 'Glyma.09G277300' => 'gma', 'Glyma.11G235600' => 'gma', 'Glyma.14G053400' => 'gma', 'Glyma.18G021300' => 'gma', 'Glyma.18G211800' => 'gma', 'Glyma.18G211900' => 'gma', 'Glyma.18G212100' => 'gma', 'Glyma.19G111400' => 'gma', 'Glyma.19G111500' => 'gma', 'Glyma.19G111700' => 'gma', 'Gohir.A02G004800' => 'ghi', 'Gohir.A02G004900' => 'ghi', 'Gohir.A05G402200' => 'ghi', 'Gohir.A06G176200' => 'ghi', 'Gohir.A10G149300' => 'ghi', 'Gohir.A10G181000' => 'ghi', 'Gohir.D02G005100' => 'ghi', 'Gohir.D02G005300' => 'ghi', 'Gohir.D04G013400' => 'ghi', 'Gohir.D06G185800' => 'ghi', 'Gohir.D10G117500' => 'ghi', 'Gohir.D10G187800' => 'ghi', 'Gorai.005G005800' => 'gra', 'Gorai.005G006000' => 'gra', 'Gorai.010G217900' => 'gra', 'Gorai.011G129400' => 'gra', 'Gorai.011G210600' => 'gra', 'Gorai.012G015700' => 'gra', 'GSVIVG01030214001' => 'vvi', 'GSVIVG01030215001' => 'vvi', 'GSVIVG01032713001' => 'vvi', 'HanXRQChr01g0000001' => 'han', 'HanXRQChr09g0251501' => 'han', 'HanXRQChr10g0286291' => 'han', 'HanXRQChr10g0298251' => 'han', 'HanXRQChr15g0493811' => 'han', 'Haze_17333' => 'cav', 'Haze_21139' => 'cav', 'Haze_21140' => 'cav', 'Haze_21145' => 'cav', 'Hma1.2p1_0118F.1_g056550' => 'hma', 'Hma1.2p1_0174F.1_g077000' => 'hma', 'Hma1.2p1_0588F.1_g184575' => 'hma', 'Hma1.2p1_1052F.1_g252360' => 'hma', 'Hma1.2p1_1240F.1_g269540' => 'hma', 'HPP92_000037' => 'vpl', 'HPP92_003706' => 'vpl', 'HPP92_006014' => 'vpl', 'HPP92_011979' => 'vpl', 'HPP92_011987' => 'vpl', 'HPP92_013825' => 'vpl', 'HPP92_013871' => 'vpl', 'HPP92_016102' => 'vpl', 'HPP92_019065' => 'vpl', 'Hund03744' => 'sun', 'Hund03784' => 'sun', 'Hund13475' => 'sun', 'Hund19801' => 'sun', 'Lalb_Chr01g0023651' => 'lal', 'Lalb_Chr04g0259291' => 'lal', 'Lalb_Chr07g0190691' => 'lal', 'Lalb_Chr10g0105421' => 'lal', 'Lalb_Chr12g0207571' => 'lal', 'Lalb_Chr12g0207581' => 'lal', 'Lalb_Chr13g0291881' => 'lal', 'Lalb_Chr19g0124081' => 'lal', 'Lalb_Chr23g0277231' => 'lal', 'Lj1A965T41' => 'lonja', 'Lj1g0017699' => 'lja', 'Lj1g0026787' => 'lja', 'Lj2A62T70' => 'lonja', 'Lj3A942T86' => 'lonja', 'Lj3C942G13' => 'lonja', 'Lj3g0009835' => 'lja', 'Lj3g0016412' => 'lja', 'Lj6g0018919' => 'lja', 'LjContig00357g0016613' => 'lja', 'Lsat_1_v5_gn_5_148221' => 'lsa', 'Lsat_1_v5_gn_8_119741' => 'lsa', 'Lsat_1_v5_gn_9_38061' => 'lsa', 'Lsat_1_v5_gn_9_59180' => 'lsa', 'Manes.07G138300' => 'mes', 'Manes.08G173200' => 'mes', 'Manes.09G115600' => 'mes', 'Manes.09G115700' => 'mes', 'Manes.10G005500' => 'mes', 'Mapoly0043s0129' => 'mpo', 'MBI02_g35825_MAGBIO' => 'mbi', 'MBI15_g26245_MAGBIO' => 'mbi', 'MBI15_g27350_MAGBIO' => 'mbi', 'MBI15_g27352_MAGBIO' => 'mbi', 'MD01G1163200' => 'mdo', 'MD04G1171400' => 'mdo', 'MD04G1171500' => 'mdo', 'MD07G1231200' => 'mdo', 'MD12G1184800' => 'mdo', 'MD12G1184900' => 'mdo', 'Medtr3g072350' => 'mtr', 'Medtr4g029040' => 'mtr', 'Medtr4g029090' => 'mtr', 'Medtr5g083980' => 'mtr', 'Medtr7g072550' => 'mtr', 'Medtr7g072560' => 'mtr', 'MELO3C009115.2' => 'cme', 'MELO3C019999.2' => 'cme', 'MELO3C026053.2' => 'cme', 'MELO3C026054.2' => 'cme', 'Migut.F00587' => 'egut', 'Migut.F01261' => 'egut', 'Migut.J00062' => 'egut', 'Migut.J00063' => 'egut', 'MSTRG.18957' => 'ama', 'MSTRG.18958' => 'ama', 'MSTRG.27279' => 'ama', 'MSTRG.5516' => 'ama', 'MSTRG.8901' => 'ama', 'Nitab4.5_0000126g0030' => 'nta', 'Nitab4.5_0000126g0040' => 'nta', 'Nitab4.5_0000263g0240' => 'nta', 'Nitab4.5_0000381g0010' => 'nta', 'Nitab4.5_0002713g0010' => 'nta', 'Nitab4.5_0002938g0010' => 'nta', 'Nitab4.5_0009418g0020' => 'nta', 'Nitab4.5_0010742g0010' => 'nta', 'Nn2g11099' => 'nnu', 'Nn2g11100' => 'nnu', 'Nn2g13335' => 'nnu', 'Nn2g13337' => 'nnu', 'Nn7g38233' => 'nnu', 'Oeu026964.1' => 'oeu', 'Oeu054430.1' => 'oeu', 'Oeu054431.1' => 'oeu', 'Oeu058655.1' => 'oeu', 'Oeu060447.2' => 'oeu', 'Oeu060448.2' => 'oeu', 'Oeu064875.2' => 'oeu', 'Oeu064876.1' => 'oeu', 'Os01g0166700' => 'osa', 'Os03g0339700' => 'osa', 'Os05g0335100' => 'osa', 'Os05g0476100' => 'osa', 'Os07g0677900' => 'osa', 'Os11g0112800' => 'osa', 'Os12g0112200' => 'osa', 'Peaxi162Scf00009g00811' => 'pax', 'Peaxi162Scf00464g00002' => 'pax', 'Peaxi162Scf00732g00440' => 'pax', 'Peaxi162Scf00732g00449' => 'pax', 'PGR004G2314' => 'pgr', 'PGR004G2520' => 'pgr', 'PGR031G0394' => 'pgr', 'PGR031G1876' => 'pgr', 'PGR142G2073' => 'pgr', 'PGSC0003DMG400026572' => 'stu', 'PGSC0003DMG400026574' => 'stu', 'PGSC0003DMG400029079' => 'stu', 'Phvul.001G249000' => 'pvu', 'Phvul.008G084700' => 'pvu', 'Phvul.008G084800' => 'pvu', 'Phvul.008G086500' => 'pvu', 'Phvul.008G218300' => 'pvu', 'Phvul.010G067400' => 'pvu', 'Phvul.010G067500' => 'pvu', 'Potri.006G107300' => 'ptr', 'Potri.016G133300' => 'ptr', 'Potri.016G133400' => 'ptr', 'Potri.019G049201' => 'ptr', 'Pp3c14_24360' => 'ppa', 'Pp3c17_22230' => 'ppa', 'PRCOL_00006315' => 'pco', 'Prupe.2G261200' => 'ppe', 'Prupe.6G289900' => 'ppe', 'Prupe.6G290000' => 'ppe', 'Psat0s207g0200' => 'psa', 'Psat3g120560' => 'psa', 'Psat3g121320' => 'psa', 'Psat5g131480' => 'psa', 'Psat7g230000' => 'psa', 'Psat7g230080' => 'psa', 'PSO339G4844' => 'pso', 'PSO384G2267' => 'pso', 'PSO384G5075' => 'pso', 'QL07p032778' => 'qlo', 'QL07p032789' => 'qlo', 'QL08p064498' => 'qlo', 'RcHm_v2.0_Chr1g0371731' => 'rch', 'RcHm_v2.0_Chr3g0460961' => 'rch', 'RcHm_v2.0_Chr3g0460971' => 'rch', 'Rhsim03G0150400' => 'rsi', 'Rhsim04G0122900' => 'rsi', 'Rhsim05G0228900' => 'rsi', 'Rhsim05G0229000' => 'rsi', 'Sabra04G0151000' => 'sbr', 'Sabra06G0083500' => 'sbr', 'Sabra19G0058700' => 'sbr', 'Sc02g0000820' => 'sci', 'Sc02g0000830' => 'sci', 'Sc10g0002870' => 'sci', 'Sed0000246' => 'sed', 'Sed0001794' => 'sed', 'Sed0009478' => 'sed', 'Sed0011321' => 'sed', 'Sed0026963' => 'sed', 'SGA_v2.0_scaffold373G50170' => 'sas', 'SGA_v2.0_scaffold60G20914' => 'sas', 'SGA_v2.0_scaffold85G26650' => 'sas', 'SHI12907' => 'shi', 'Solyc06g050350.3' => 'sly', 'Solyc09g042700.4' => 'sly', 'Solyc09g042710.3' => 'sly', 'Solyc10g085430.3' => 'sly', 'Sopen06g015840' => 'spe', 'Sopen09g015490' => 'spe', 'Sopen09g015510' => 'spe', 'Sopen10g034880' => 'spe', 'Sp4g20690' => 'spa', 'Sp4g22830' => 'spa', 'Sp5g06230' => 'spa', 'Sp5g10550' => 'spa', 'Sp5g10560' => 'spa', 'Sp6g41050' => 'spa', 'Sp7g08830' => 'spa', 'TAR623G0962' => 'tar', 'TAR623G1430' => 'tar', 'TAR627G0090' => 'tar', 'TAR629G1123' => 'tar', 'TAR636G1426' => 'tar', 'THA.LOC104803194' => 'tha', 'THA.LOC104806073' => 'tha', 'THA.LOC104806079' => 'tha', 'THA.LOC104806629' => 'tha', 'THA.LOC104823315' => 'tha', 'THA.LOC104824518' => 'tha', 'Thecc.04G154900' => 'tca', 'Thecc.04G155100' => 'tca', 'Thecc.10G175000' => 'tca', 'Thhalv10005963m.g' => 'esa', 'Thhalv10009793m.g' => 'esa', 'Thhalv10010401m.g' => 'esa', 'Thhalv10010716m.g' => 'esa', 'Thhalv10014673m.g' => 'esa', 'Thhalv10016492m.g' => 'esa', 'Thhalv10016518m.g' => 'esa', 'TPR.G1794' => 'tpr', 'TPR.G20215' => 'tpr', 'TPR.G29582' => 'tpr', 'TPR.G31629' => 'tpr', 'TPR.G4407' => 'tpr', 'TPR.G4415' => 'tpr', 'TPR.G4963' => 'tpr', 'TPR.G5005' => 'tpr', 'TWI53G0639' => 'twi', 'TWI53G1003' => 'twi', 'TWI73G0435' => 'twi', 'TWI74G0479' => 'twi', 'TWI74G1328' => 'twi', 'TWI77G0311' => 'twi', 'TWI77G0482' => 'twi', 'unitig_0.g257' => 'ugi', 'unitig_2.g29668' => 'ugi', 'unitig_27.g24880' => 'ugi', 'unitig_46.g18742' => 'ugi', 'unitig_62.g23925' => 'ugi', 'unitig_699.g19371' => 'ugi', 'unitig_747.g21402' => 'ugi', 'unitig_8.g3220' => 'ugi', 'vmacro08930' => 'vma', 'vmacro20355' => 'vma', 'vmacro20356' => 'vma', 'vmacro23407' => 'vma', 'VMungo0251G1611' => 'vmu', 'VMungo0331G1084' => 'vmu', 'VMungo0331G1328' => 'vmu', 'VMungo0647G1783' => 'vmu', 'VMungo1383G1340' => 'vmu', 'VMungo1383G1499' => 'vmu', 'VMungo1383G2320' => 'vmu', 'VMungo1383G3549' => 'vmu', 'Zm00001eb035560' => 'zma', 'Zm00001eb111490' => 'zma', 'Zm00001eb123280' => 'zma', 'Zm00001eb163980' => 'zma', 'Zm00001eb167030' => 'zma', 'Zm00001eb168900' => 'zma', 'Zm00001eb318120' => 'zma', 'Zm00001eb350240' => 'zma', 'Zm00001eb351980' => 'zma', 'Zm00001eb395070' => 'zma', 'Zm00001eb406340' => 'zma', 'Zm00001eb423520' => 'zma' ) $gf_id = 'HOM05D001122' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001122' ) $data_identifier = 'HOM05D001122' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 27, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 6, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 32, 'bol' => (int) 16, 'bra' => (int) 10, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 6, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 3, 'csa' => (int) 7, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 17, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 3, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 7, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 8, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 8, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423520' $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